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Gene ID/Symbol/Name (e.g., LOC_Os01g08570 or hwh1 or Os01g0180900 or gly%ltransferase, note: wildcard character '%' is also acceptable.):
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Search Results:

43 variations found. LOC_Os09g10310 (retrotransposon protein; putative; Ty3-gypsy subclass), ranging from 5,620,904 bp to 5,621,529 bp (including 0 kb upstream and 0 kb downstream of the gene).

Variation Map (with Chromatin Accessibility Map/ Non-coding Varation Scores Map) in Searched Region:

The 'big effect' variations are marked out:

ColorExplainDetails
red High impact variants defined by snpEff 'STOP_LOST', 'START_LOST', 'STOP_GAINED', 'FRAME_SHIFT' et. al., the details can be found at http://snpef f.sourceforge.net/SnpEff_manual.html#eff.
purple 'Damaging' or 'probably damaging' non-synonymous SNPs defined by PolyPhen-2 This is a qualitative result of nonsynonymous SNP annotation, where 'damaging' or 'probably damaging' means that the variant is more likely to affect protein function. Details can be found here.

Detailed Variation Information:

Var ID Chrom Position Primary Allele Secondary Allele Primary Allele Frequency DEL Frequency Var GWAS Results Effect
vg0905620913 (J) chr09 5620913 G A 99.80% 0.00% G -> A NA
LOC_Os09g10310.1 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os09g10320.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)
LOC_Os09g10330.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 48.643; most accessible tissue: Zhenshan97 flag leaf, score: 64.768
vg0905620923 (J) chr09 5620923 G A 98.80% 0.00% G -> A NA
LOC_Os09g10310.1 Alt: A| synonymous_variant LOW(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 49.638; most accessible tissue: Zhenshan97 flag leaf, score: 66.824
vg0905620924 (J) chr09 5620924 G A 65.70% 5.23% A -> G
mr1034 (All); LR P-value: 2.96E-12;
mr1163 (All); LR P-value: 4.29E-22;
mr1700_2 (All); LR P-value: 9.62E-08
LOC_Os09g10310.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os09g10310.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 49.692; most accessible tissue: Zhenshan97 flag leaf, score: 66.824
vg0905620942 (J) chr09 5620942 TCTTCCT CTGGAAT AGCTGGC TCTC T 97.90% 0.00% TCTTCCTCTG GAATAGCTGG CTCTC -> T NA
LOC_Os09g10310.1 Alt: T| disruptive_inframe_deletion MODERATE(snpEff)
LOC_Os09g10320.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)
LOC_Os09g10330.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 52.930; most accessible tissue: Zhenshan97 flag leaf, score: 65.820
vg0905620951 (J) chr09 5620951 G T 97.80% 0.00% G -> T,GGT NA
LOC_Os09g10310.1 Alt: GGT| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
LOC_Os09g10310.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 53.533; most accessible tissue: Zhenshan97 flag leaf, score: 66.327
vg0905620954 (J) chr09 5620954 A G 94.30% 2.48% A -> G NA
LOC_Os09g10310.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os09g10310.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 53.558; most accessible tissue: Zhenshan97 flag leaf, score: 67.310
vg0905620966 (J) chr09 5620966 T C 50.70% 0.00% C -> T NA
LOC_Os09g10310.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 53.737; most accessible tissue: Zhenshan97 flag leaf, score: 68.250
vg0905620973 (J) chr09 5620973 C T 97.80% 0.00% C -> T NA
LOC_Os09g10310.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 52.628; most accessible tissue: Zhenshan97 flag leaf, score: 67.310
vg0905620990 (J) chr09 5620990 G A 93.40% 0.00% G -> A
mr1064 (Jap_All); LR P-value: 9.91E-06;
mr1826_2 (All); LR P-value: 9.68E-06
LOC_Os09g10310.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 53.689; most accessible tissue: Zhenshan97 flag leaf, score: 70.837
vg0905620992 (J) chr09 5620992 G A 97.80% 0.00% G -> A NA
LOC_Os09g10310.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 53.184; most accessible tissue: Zhenshan97 flag leaf, score: 70.837
vg0905621005 (J) chr09 5621005 G A 94.30% 0.00% G -> A NA
LOC_Os09g10310.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 53.415; most accessible tissue: Zhenshan97 flag leaf, score: 70.425
vg0905621013 (J) chr09 5621013 T A 98.20% 0.00% T -> A NA
LOC_Os09g10310.1 Alt: A| synonymous_variant LOW(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 53.910; most accessible tissue: Zhenshan97 flag leaf, score: 71.238
vg0905621014 (J) chr09 5621014 C A 98.20% 0.00% C -> A NA
LOC_Os09g10310.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 53.910; most accessible tissue: Zhenshan97 flag leaf, score: 71.238
vg0905621024 (J) chr09 5621024 C T 98.80% 0.00% C -> T NA
LOC_Os09g10310.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 54.946; most accessible tissue: Zhenshan97 flag leaf, score: 72.757
vg0905621034 (J) chr09 5621034 C G 96.50% 0.00% C -> G NA
LOC_Os09g10310.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 54.858; most accessible tissue: Zhenshan97 flag leaf, score: 72.012
vg0905621055 (J) chr09 5621055 G T 99.10% 0.00% G -> T NA
LOC_Os09g10310.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
The average chromatin accessibility score: 54.013; most accessible tissue: Zhenshan97 flag leaf, score: 70.837
vg0905621061 (J) chr09 5621061 C T 69.70% 0.00% T -> C
mr1323 (All); LR P-value: 2.83E-16;
mr1700_2 (All); LR P-value: 6.71E-08
LOC_Os09g10310.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 55.000; most accessible tissue: Zhenshan97 flag leaf, score: 70.837
vg0905621113 (J) chr09 5621113 T C 72.50% 0.00% C -> T
mr1163 (All); LR P-value: 1.78E-22;
mr1700_2 (All); LR P-value: 7.21E-08
LOC_Os09g10310.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 53.943; most accessible tissue: Zhenshan97 flag leaf, score: 70.425
vg0905621124 (J) chr09 5621124 G A 99.10% 0.00% G -> A NA
LOC_Os09g10310.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 54.016; most accessible tissue: Zhenshan97 young leaf, score: 69.723
vg0905621125 (J) chr09 5621125 C T 94.30% 0.00% C -> T NA
LOC_Os09g10310.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 54.098; most accessible tissue: Zhenshan97 young leaf, score: 70.625
vg0905621166 (J) chr09 5621166 T C 54.80% 0.00% C -> T NA
LOC_Os09g10310.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 54.185; most accessible tissue: Zhenshan97 young leaf, score: 69.723
vg0905621214 (J) chr09 5621214 C T 98.80% 0.00% C -> T NA
LOC_Os09g10310.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 53.940; most accessible tissue: Zhenshan97 flag leaf, score: 69.582
vg0905621216 (J) chr09 5621216 G A 94.20% 0.00% G -> A NA
LOC_Os09g10310.1 Alt: A| stop_gained HIGH(snpEff)/stop_gained(CooVar)
The average chromatin accessibility score: 54.139; most accessible tissue: Zhenshan97 flag leaf, score: 70.425
vg0905621224 (J) chr09 5621224 G A 69.70% 0.00% A -> G
mr1299_2 (All); LR P-value: 3.25E-08;
mr1645_2 (All); LR P-value: 6.64E-08;
mr1700_2 (All); LR P-value: 1.01E-08;
mr1727_2 (All); LR P-value: 9.04E-07
LOC_Os09g10310.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 53.249; most accessible tissue: Zhenshan97 flag leaf, score: 68.250
vg0905621237 (J) chr09 5621237 A G 53.60% 0.00% G -> A NA
LOC_Os09g10310.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 52.237; most accessible tissue: Zhenshan97 flag leaf, score: 67.310
vg0905621248 (J) chr09 5621248 A T 69.70% 0.00% T -> A
mr1299_2 (All); LR P-value: 3.25E-08;
mr1645_2 (All); LR P-value: 6.64E-08;
mr1700_2 (All); LR P-value: 1.01E-08;
mr1727_2 (All); LR P-value: 9.04E-07
LOC_Os09g10310.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 51.555; most accessible tissue: Zhenshan97 flag leaf, score: 66.327
vg0905621270 (J) chr09 5621270 T C 53.60% 0.00% C -> T NA
LOC_Os09g10310.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 52.171; most accessible tissue: Zhenshan97 young leaf, score: 67.830
vg0905621362 (J) chr09 5621362 G A 94.30% 0.00% G -> A NA
LOC_Os09g10310.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 44.224; most accessible tissue: Zhenshan97 flag leaf, score: 63.101
vg0905621369 (J) chr09 5621369 C A 99.10% 0.00% C -> A,T NA
LOC_Os09g10310.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os09g10320.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)
LOC_Os09g10330.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)
LOC_Os09g10310.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
The average chromatin accessibility score: 43.375; most accessible tissue: Zhenshan97 flag leaf, score: 61.926
vg0905621375 (J) chr09 5621375 G A 94.30% 0.00% G -> A NA
LOC_Os09g10310.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
The average chromatin accessibility score: 42.905; most accessible tissue: Zhenshan97 flag leaf, score: 61.322
vg0905621406 (J) chr09 5621406 A G 97.70% 0.00% A -> G NA
LOC_Os09g10310.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 41.722; most accessible tissue: Zhenshan97 flag leaf, score: 59.429
vg0905621407 (J) chr09 5621407 T C 92.40% 0.00% T -> C NA
LOC_Os09g10310.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 41.722; most accessible tissue: Zhenshan97 flag leaf, score: 59.429
vg0905621409 (J) chr09 5621409 C T 94.30% 0.00% C -> T NA
LOC_Os09g10310.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 41.353; most accessible tissue: Zhenshan97 flag leaf, score: 59.429
vg0905621415 (J) chr09 5621415 A G 82.40% 0.00% A -> G NA
LOC_Os09g10310.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 39.814; most accessible tissue: Zhenshan97 flag leaf, score: 58.104
vg0905621423 (J) chr09 5621423 C T 99.10% 0.00% C -> T NA
LOC_Os09g10310.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
The average chromatin accessibility score: 37.834; most accessible tissue: Zhenshan97 flag leaf, score: 54.545
vg0905621427 (J) chr09 5621427 G T 97.70% 0.00% G -> T NA
LOC_Os09g10310.1 Alt: T| synonymous_variant LOW(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
The average chromatin accessibility score: 39.371; most accessible tissue: Callus, score: 57.912
vg0905621428 (J) chr09 5621428 G T 97.70% 0.00% G -> T,A NA
LOC_Os09g10310.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
LOC_Os09g10310.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 39.451; most accessible tissue: Callus, score: 57.912
vg0905621431 (J) chr09 5621431 A G 94.30% 0.00% A -> G NA
LOC_Os09g10310.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 39.272; most accessible tissue: Callus, score: 57.912
vg0905621452 (J) chr09 5621452 A T 99.10% 0.00% A -> T NA
LOC_Os09g10310.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
The average chromatin accessibility score: 39.002; most accessible tissue: Callus, score: 57.912
vg0905621453 (J) chr09 5621453 T C 94.30% 0.00% T -> C NA
LOC_Os09g10310.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 39.002; most accessible tissue: Callus, score: 57.912
vg0905621455 (J) chr09 5621455 T C 99.00% 0.00% T -> C NA
LOC_Os09g10310.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 38.941; most accessible tissue: Callus, score: 57.912
vg0905621475 (J) chr09 5621475 T C 53.60% 0.00% C -> T NA
LOC_Os09g10310.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 36.062; most accessible tissue: Callus, score: 57.912
vg0905621505 (J) chr09 5621505 C T 72.50% 0.00% T -> C NA
LOC_Os09g10310.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 35.165; most accessible tissue: Callus, score: 57.912